Re: minimise in restarting first equilibration step

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 13 2020 - 12:54:03 CDT

Hello Asma, adding to what Josh already described: NAMD will keep running
regardless of whether minimization criteria have been fulfilled or not.
You should be aware of this because a minimization criterion is actually
not given by you (did you give one?), and there is no default one:
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node34.html

Other MD codes have a built-in decision, which stops the run and prints a
message if the minimization has been "completed". NAMD by design lets you
decide when you have reached a local minimum: all energy terms are printed
with several digits of precision in the standard output.

Was this the problem? If not, it'd be hard to tell given the few details.

Giacomo

On Mon, Apr 13, 2020 at 1:43 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> Hi Asma,
>
>
> Maybe I wasn't clear enough the first time, but you only put minimize in
> the configuration file when you want to minimize. If you've already started
> doing dynamics after minimizing in the first part of equilibration, you
> wouldn't want to start minimizing again, would you? I would take it out if
> the minimization steps have already completed.
>
>
> -Josh
>
>
> On 4/13/20 11:24 AM, Khoualdi Asma Feriel wrote:
>
> Hello,
>
> Thank you for your reply.
> To clarify, I am not yet done with step 1, it is continuing it. That is
> why I am not sure if system is done minimising or not and, consequently,
> should I keep minimise command when using restart files of first
> equilibration step and resuming this first equilibration step?
>
> Thank you.
>
> Asma Feriel
>
> Get Outlook for iOS <https://aka.ms/o0ukef>
> ------------------------------
> *From:* Josh Vermaas <yoshi121212_at_gmail.com> <yoshi121212_at_gmail.com> on
> behalf of Josh Vermaas <joshua.vermaas_at_gmail.com>
> <joshua.vermaas_at_gmail.com>
> *Sent:* Monday, April 13, 2020 1:16:35 PM
> *To:* namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu>;
> Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca>
> <asma.feriel.khoualdi_at_umontreal.ca>
> *Subject:* Re: namd-l: minimise in restarting first equilibration step
>
>
> Hi Asma,
>
>
> Not unless you want to minimize something after dynamics has started
> (unlikely). The minimize command should only be active when you want to do
> minimization, which is usually only the very first equilibration step.
>
>
> -Josh
>
>
> On 4/13/20 8:37 AM, Khoualdi Asma Feriel wrote:
>
> Hello,
>
> since the first equilibration step was stopped on hitting wall time
> without finishing, I want to use restart files to resume it. Since it is
> the first step, should I keep the minimize option in namd configuration
> file?
>
>
> Best,
>
> Asma Feriel
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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